Very glad to hear that.Holy crap, transposing a couple of things an octave or two around after adding highpass filters on everything and adjusting/adding some lowpass on some other things (to weed out any frequencies out of their audible range) has done wonders to make everything sound more distinct.
Also, one person once told me to use one or two shelves rather than a steep filter, and it currently works much better for me; maybe you could try it, too.
For a guitar clipping, you can try to lower gain early in your chain and then compensate; also check if your sound is okay a) in mono and b) with Side channel muted. Muting built-in synth effects, if any, could also help to locate the problem.
Best of luck.